diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 | ||||
| -rw-r--r-- | gnu/packages/patches/delly-use-system-libraries.patch | 56 |
3 files changed, 20 insertions, 77 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index c76908f92f..d155b4c613 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -642,7 +642,6 @@ dist_patch_DATA = \ %D%/packages/patches/datamash-arm-tests.patch \ %D%/packages/patches/dbus-helper-search-path.patch \ %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \ - %D%/packages/patches/delly-use-system-libraries.patch \ %D%/packages/patches/dfu-programmer-fix-libusb.patch \ %D%/packages/patches/diffutils-gets-undeclared.patch \ %D%/packages/patches/diffutils-getopt.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc21848367..78debbc873 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2155,42 +2155,42 @@ identify enrichments with functional annotations of the genome.") (define-public delly (package (name "delly") - (version "0.7.7") + (version "0.7.9") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/tobiasrausch/delly/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dellytools/delly.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) - (patches (search-patches "delly-use-system-libraries.patch")))) + (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/htslib") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. - #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:make-flags + (list "PARALLEL=1" ; Allow parallel execution at run-time. + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda _ - (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) - (templates (string-append (assoc-ref %outputs "out") + (add-after 'install 'install-templates + (lambda* (#:key outputs #:allow-other-keys) + (let ((templates (string-append (assoc-ref outputs "out") "/share/delly/templates"))) - (mkdir-p bin) (mkdir-p templates) (copy-recursively "excludeTemplates" templates) - (install-file "src/cov" bin) - (install-file "src/delly" bin) - (install-file "src/dpe" bin))))))) - (native-inputs - `(("python" ,python-2))) + #t)))))) (inputs `(("boost" ,boost) ("htslib" ,htslib) ("zlib" ,zlib) ("bzip2" ,bzip2))) - (home-page "https://github.com/tobiasrausch/delly") + (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch deleted file mode 100644 index 3315c2a176..0000000000 --- a/gnu/packages/patches/delly-use-system-libraries.patch +++ /dev/null @@ -1,56 +0,0 @@ ---- a/Makefile 2017-04-09 12:48:15.000000000 +0200 -+++ b/Makefile 2017-06-21 14:26:02.749282787 +0200 -@@ -9,8 +9,8 @@ - - # Flags - CXX=g++ --CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing --LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time - - # Additional flags for release/debug - ifeq (${PARALLEL}, 1) -@@ -23,7 +23,7 @@ - ifeq (${STATIC}, 1) - LDFLAGS += -static -static-libgcc -pthread -lhts -lz - else -- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib -+ LDFLAGS += -lhts -lz - endif - ifeq (${DEBUG}, 1) - CXXFLAGS += -g -O0 -fno-inline -DDEBUG -@@ -41,29 +41,17 @@ - DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) - - # Targets --TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe -+TARGETS = src/delly src/cov src/dpe - - all: $(TARGETS) - --.htslib: $(HTSLIBSOURCES) -- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib -- --.bcftools: $(HTSLIBSOURCES) -- cd src/bcftools && make && cd ../../ && touch .bcftools -- --.boost: $(BOOSTSOURCES) -- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost -- --src/delly: .htslib .bcftools .boost $(DELLYSOURCES) -- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -- --src/cov: .htslib .bcftools .boost $(DELLYSOURCES) -+src/cov: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/dpe: .htslib .bcftools .boost $(DELLYSOURCES) -+src/dpe: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - - clean: - cd src/htslib && make clean - cd src/modular-boost && ./b2 --clean-all -- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools -+ rm -f $(TARGETS) $(TARGETS:=.o) |